From ef7fe8f34f679c243ba2fa0ce0d3a2e678181f7d Mon Sep 17 00:00:00 2001
From: jrobinso <jrobinso@broadinstitute.org>
Date: Wed, 21 Jul 2021 08:52:17 -0700
Subject: [PATCH] Add default filters to CRAM decoder (including filter
 duplicates).   Fixes #1323

---
 js/cram/cramReader.js | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/js/cram/cramReader.js b/js/cram/cramReader.js
index 683c190cd..f593ceabe 100644
--- a/js/cram/cramReader.js
+++ b/js/cram/cramReader.js
@@ -149,6 +149,7 @@ class CramReader {
                 const records = await this.indexedCramFile.getRecordsForRange(chrIdx, bpStart, bpEnd);
 
                 for (let record of records) {
+
                     const refID = record.sequenceId;
                     const pos = record.alignmentStart;
                     const alignmentEnd = pos + record.lengthOnRef;
@@ -166,9 +167,9 @@ class CramReader {
 
                     const alignment = decodeCramRecord(record, header.chrNames);
 
-                    //  if (filter.pass(alignment)) {
-                    alignmentContainer.push(alignment);
-                    //  }
+                    if (this.filter.pass(alignment)) {
+                        alignmentContainer.push(alignment);
+                    }
                 }
 
                 alignmentContainer.finish();